RetrogeneDB ID: retro_cjac_4087

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:71049644..71050489(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CDCA7
• Ensembl ID: ENSCJAG00000007809
• Aliases: None
• Description: cell division cycle associated 7 [Source:HGNC Symbol;Acc:14628]

Sequence

>retro_cjac_4087
TCTCAGAGTGAGATACAAGATGGAATGAGGCTGCAGTCAGTTCGGGAAGGCTGTAAGACCCACAGCCAGTGCAGGCACTC
TGGCCTCTCAGGGTGGTGATGAAGTTTCCAGCACGAAGTACCAGGGGAGCAACCAACAAAAAACAGAGCCCCGCTCCCCA
CCCCCAGCCCTCAGAGCATTCTGTAACTGATTGCAACTCCAATTCAGAAGATTAAAGTGGGATGAATTTTTTGGAGAAAA
GGGATTTAAATATAAAGCAAAACAAAGCAATGCTTGCAAAACTCATGTCTGAATTTGAAAGCTTCCCTGGCTCATTCCCT
GGAAGACCTTCCTTCCCAGCCTCAAACTCACAATCAAGGAGACTGTGAAGGCATACATTCCCAGGTGTTGCATCCAGGAG
AAGTCCTGAACAGAGAGCTCGTCCTCTTATCAGGTCAAGGTCCCAGATCCTCAGGTCTGCTGATGCTCTACCCATGGAGG
AGAATGAGGAAGAGGATAAGTACATGTTGGTGAAAAAGAGGAAGACCATGAATGGTTACATGAACAAAAATGACACACCC
AGGAATCATCATTCCGGATCATCCATGGCCCTTCAGCATATAATTCACCCAGTGGAAGAAATTACAGAGGAAGAACTGGA
GAACATCTGCAGCAACTCTAGATAGAAGCTATATAACCGTGCACTGGGCTCTACTTGTCATCAAGGCCATCAGAATACTA
TTGATACCAAAACAAACTGCAGAAACCCAGACTGCTGGAGTGTTCCAGGACAGTTCTGCCTCCCCTGCCTTCGAAACTGT
TATGGTGAAGAGGTCAGGGATGCTCTCCTGCATCCGAACTGGCAT

Alignment

ORF - retro_cjac_4087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.82 %
• Parental protein coverage: 62.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SESEIQDGMRLQSVREGCRTRSQCRHSG-PLRVAMKFPARSTRGATNKK---AELPQSSENSVTDSDSDS
          S.SEIQDGMRLQSVREGC.T.SQCRHSG.PLRV.MKFPARSTRGATNKK...A..PQ.SE.SVTD..S.S
Retrocopy SQSEIQDGMRLQSVREGCKTHSQCRHSG<PLRVVMKFPARSTRGATNKKQSPAPHPQPSEHSVTDCNSNS

Parental  EDESGMNFLEKRALNIKQNKAMLAKLMSELESFPGSFPGRHSLPGSNSQSRRPRRRTFPGVASRRNPERR
          ED.SGMNFLEKR.LNIKQNKAMLAKLMSE.ESFPGSFPGR.S.P.SNSQSRR..R.TFPGVASRR.PE.R
Retrocopy ED*SGMNFLEKRDLNIKQNKAMLAKLMSEFESFPGSFPGRPSFPASNSQSRRL*RHTFPGVASRRSPEQR

Parental  ARPLTRSRSRILGSVDTLPMEEEEEEEDKYMLVRKRKTMDSYVNEDDMPRSRRCRSSLTLPHIIRPVEEI
          ARPL.RSRS.IL.S.D.LPMEE.EEE.DKYMLV.KRKTM..Y.N..D.PR.....SS..L.HII.PVEEI
Retrocopy ARPLIRSRSQILRSADALPMEENEEE-DKYMLVKKRKTMNGYMNKNDTPRNHHSGSSMALQHIIHPVEEI

Parental  TEEDLENICSSSREKIYNRSLGSTCHQCRQKTIDTKTNCRNPDCCGVRGQFCGPCLRNRYGEEVRDALLD
          TEE.LENICS.SR.K.YNR.LGSTCHQ..Q.TIDTKTNCRNPDC..V.GQFC.PCLRN.YGEEVRDALL.
Retrocopy TEEELENICSNSR*KLYNRALGSTCHQGHQNTIDTKTNCRNPDCWSVPGQFCLPCLRNCYGEEVRDALLH

Parental  PNWH
          PNWH
Retrocopy PNWH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	11.18 RPM
SRP051959_heart	0.00 RPM	2.46 RPM
SRP051959_kidney	0.00 RPM	4.39 RPM
SRP051959_liver	0.00 RPM	1.28 RPM
SRP051959_lung	0.00 RPM	8.31 RPM
SRP051959_lymph_node	0.00 RPM	9.04 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.48 RPM
SRP051959_spleen	0.00 RPM	5.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4087 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087 ,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,